Streams are vital components of landscapes, providing essential ecosystem services such as nutrient cycling, biodiversity support, and habitat connectivity. However, agricultural intensification, land-use change, and climate variability continue to threaten their ecological integrity. Effective biomonitoring is therefore critical for maintaining water quality and sustaining aquatic biodiversity. Traditional morphology-based identification of macroinvertebrates (e.g., Ephemeroptera, Plecoptera, and Trichoptera) remains central to freshwater bioassessment but is constrained by the need for taxonomic expertise, time-intensive processing, and limited detection sensitivity. High-throughput sequencing technologies, including DNA metabarcoding of bulk tissue and environmental DNA (eDNA), can overcome many of these limitations. This ongoing study integrates morphology-based identification with DNA metabarcoding to evaluate stream health across impacted and reference sites within the Ochlockonee River Basin in southwest Georgia and northwest Florida. Both bulk macroinvertebrate and eDNA water samples were analyzed using the cytochrome oxidase I (COI) gene primers (mlCOIintF/jgHCO2198). Physicochemical parameters (dissolved oxygen, turbidity, pH, among others) were also measured at each site. Preliminary results indicate the detection of 8 families and 17 genera of Ephemeroptera (5 families, 9 genera), Plecoptera (1 family, 5 genera), and Trichoptera (2 families, 3 genera) across study sites. Morphology-based identification recovered a greater number of taxa than DNA metabarcoding, while molecular approaches provided faster processing times and finer taxonomic resolution, revealing community differences between impacted and reference streams. Leptoceridae were detected exclusively at reference sites, whereas Leptophlebiidae were observed only at impacted sites, highlighting biodiversity patterns associated with stream condition. These findings highlight the value of integrating DNA-based and traditional approaches in freshwater biomonitoring. Combining molecular precision with established morphology-based frameworks enhances accuracy, reduces processing time, and uncovers hidden biodiversity, strengthening data-driven water quality management and aquatic conservation efforts.